Organisms from all kingdoms of life use photoreceptors to constantly monitor their light environment and regulate their behavior and development accordingly. All known biological photoreceptors are formed by a molecular team consisting of a bound organic molecule (called the chromophore) and a protein component. The chromophore absorbs the light and as a result undergoes a defined photochemical reaction. The change in the chromophore is then sensed by the protein component and translated into a protein structural change that then in turn activates a signal transduction cascade. While this general scheme is well known for a long time, the molecular details of this process have not been well understood. Photoactive Yellow Protein is a small bacterial photoreceptor that has proven to be very amenable to structural and biophysical studies and therefore offers the opportunity to ivestigate the light driven signaling process of a biological photoreceptor in molecular detail. Combination of a novel cryo-trapping strategy with sub E X-ray diffraction allowed us to determine the structure of a very shortlived, early intermediate in the light cycle of the bacterial light sensor Photoactive Yellow Protein. This structure shows for the first time, how rapid chromophore isomerization can occur in the interior of a receptor protein and suggests how the protein uses the absorbed photon to drive the remaining signaling cycle. The insights gained do not only drive our basic understanding of an important biological function but might also help us design protein based light sensors for biotechnological applications.